SMTL ID : 8zel.1

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.142, H.144, E.183, H.395 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.142, A:E.183, A:H.395, H2O.1 ZN.2: 6 residues within 4Å: Chain A: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.142, A:H.144, A:H.207, H2O.1, H2O.1 ZN.6: 5 residues within 4Å: Chain B: C.142, H.144, E.183, H.395 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.142, B:E.183, B:H.395, H2O.4 ZN.7: 6 residues within 4Å: Chain B: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.142, B:H.144, B:H.207, H2O.4, H2O.5 ZN.11: 5 residues within 4Å: Chain C: C.142, H.144, E.183, H.395 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.142, C:E.183, C:H.395, H2O.8 ZN.12: 6 residues within 4Å: Chain C: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.142, C:H.144, C:H.207, H2O.8, H2O.9 ZN.16: 5 residues within 4Å: Chain D: C.142, H.144, E.183, H.395 Ligands: ZN.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.142, D:E.183, D:H.395, H2O.12 ZN.17: 6 residues within 4Å: Chain D: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.142, D:H.144, D:H.207, H2O.12, H2O.12

4 x ORN: L-ornithine(Non-covalent)

ORN.3: 7 residues within 4Å: Chain A: E.182, E.183, D.184, E.221, R.294, F.332, S.369 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.332 Hydrogen bonds: A:E.182, A:E.183, A:E.221, A:R.294 ORN.8: 7 residues within 4Å: Chain B: E.182, E.183, D.184, E.221, R.294, F.332, S.369 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.332 Hydrogen bonds: B:E.182, B:E.183, B:E.221, B:R.294 ORN.13: 7 residues within 4Å: Chain C: E.182, E.183, D.184, E.221, R.294, F.332, S.369 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.332 Hydrogen bonds: C:E.182, C:E.183, C:E.221, C:R.294 ORN.18: 7 residues within 4Å: Chain D: E.182, E.183, D.184, E.221, R.294, F.332, S.369 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.332 Hydrogen bonds: D:E.182, D:E.183, D:E.221, D:R.294

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 1 residues within 4Å: Chain A: E.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.47 TRS.9: 1 residues within 4Å: Chain B: E.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.47 TRS.14: 1 residues within 4Å: Chain C: E.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.47 TRS.19: 1 residues within 4Å: Chain D: E.47 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.47

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 6 residues within 4Å: Chain A: F.259, K.307 Chain D: L.243, A.318, S.319, G.320 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.243 Salt bridges: A:K.307 ACY.10: 6 residues within 4Å: Chain B: F.259, K.307 Chain C: L.243, A.318, S.319, G.320 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:K.307 Hydrophobic interactions: C:L.243 ACY.15: 6 residues within 4Å: Chain B: L.243, A.318, S.319, G.320 Chain C: F.259, K.307 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.243 Salt bridges: C:K.307 ACY.20: 6 residues within 4Å: Chain A: L.243, A.318, S.319, G.320 Chain D: F.259, K.307 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:K.307 Hydrophobic interactions: A:L.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, K. et al., Crystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine. To Be Published

Release Date

2025-05-14

Peptides

Xaa-Arg dipeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xaa-Arg dipeptidase

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